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  <title>MRtrix #VERSION# documentation</title>
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  <tr>
    <td><a href="../install/index.html"><img src="../left.png"></a></td>
    <td><a href="../index.html"><img src="../up.png"></a></td>
    <td><a href="../index.html"><img src="../home.png"></a></td>
    <th>General information</th>
    <td><a href="overview.html"><img src="../right.png"></a></td>
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<ul class=toc>
  <li><a href='overview.html'>Overview</a></li>
  <ul>
    <li><a href="overview.html#cmdline">Command-line example</a></li>
    <li><a href="overview.html#mrview">MRView - the MRtrix viewer</a></li>
    <li><a href="overview.html#axes">Coordinate system</a></li>
    <li><a href="overview.html#features">Other features</a></li>
  </ul>
  <li><a href='cmdline.html'>Command line usage</a></li>
  <ul>
    <li><a href="cmdline.html#basicusage">Basic usage</a></li>
    <li><a href="cmdline.html#options">Command line options</a></li>
    <li><a href="cmdline.html#stdoptions">Standard options</a></li>
    <li><a href="cmdline.html#sequences">Number sequences</a></li>
    <li><a href="cmdline.html#pipes">Data pipes</a></li>
  </ul>
  <li><a href='formats.html'>Supported file formats and data types</a></li>
  <ul>
    <li><a href='formats.html#formats'>Supported image file formats</a></li>
    <ul>
      <li><a href='formats.html#DICOM'>DICOM</a></li>
      <li><a href='formats.html#NIfTI'>NIfTI 1.1 (*.nii)</a></li>
      <li><a href='formats.html#AVW'>Analyse/SPM (*.hdr/*.img)</a></li>
      <li><a href='formats.html#MRtrix'>MRtrix (*.mif or *.mih)</a></li>
      <li><a href='formats.html#XDS'>XDS (*.hdr/*.bfloat or *.hdr/*.bshort)</a></li>
      <!-- <li><a href='formats.html#Siemens'>Siemens Vision (*.ima)</a></li>
      <li><a href='#formats.htmlInterFile'>InterFile (*.HDR/*.IMG)</a></li> -->
      <li><a href='#formats.htmlMRTools_old'>Legacy MRTools (*.mri)</a></li>
    </ul>
    <li><a href='formats.html#datatypes'>Supported data types</a></li>
    <li><a href='formats.html#dataorder'>Data ordering</a></li>
  </ul>
  <li><a href='mrview.html'>MRView</a></li>
    <ul>
      <li><a href='mrview.html#ref'>Quick reference</a></li>
      <li><a href='mrview.html#display'>Displaying images</a></li>
      <ul>
        <li><a href='mrview.html#access'>Accessing images</a></li>
        <li><a href='mrview.html#navigate'>Navigating through the image</a></li>
        <li><a href='mrview.html#window'>Windowing the image</a></li>
      </ul>
      <li><a href='mrview.html#multi'>Displaying multiple images</a></li>
      <li><a href='mrview.html#dragdrop'>Copying the position of the focus into other applications</a></li>
      <li><a href='mrview.html#sidebar'>Additional tools: the sidebar</a></li>
      <ul>
        <li><a href='mrview.html#tractography'>Tractography</a></li>
        <li><a href='mrview.html#roi'>ROI analysis</a></li>
        <li><a href='mrview.html#overlay'>Overlay</a></li>
        <li><a href='mrview.html#orientation_plot'>Orientation plot</a></li>
        <li><a href='mrview.html#screengrab'>Screen capture</a></li>
      </ul>
  </ul>
</ul>

<p class=footer>
Donald Tournier<br>
MRtrix version #VERSION#<br>
Last updated #MTIME#
</p>


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